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The <i>CDPK</i> family genes play crucial roles in signal transduction pathways during plant development and stress response. In this study, we comprehensively analyzed the <i>CDPK</i> family genes in mustard (<i>Brassica juncea</i> L.), resulting in the identification of 101 genes (<i>BjuCDPK1</i>–<i>101</i>) located on chromosomes AA_Chr01 to BB_Chr08. RNA-seq analysis showed that most <i>BjuCDPK</i> genes were predominantly expressed in the root and flower bud, suggesting their organ-specific expression patterns. Furthermore, the expression levels of most <i>BjuCDPK</i> genes were significantly altered by cold stress. The promoter regions of <i>BjuCDPK</i> genes had abundant cis-acting elements related to hormones and stress. The interaction network analysis predicted that BjuCDPK proteins respond to abiotic stress probably via interaction with ABF1, ABF4, and/or DI19. Our findings provide valuable information for further the investigation of the cold stress adaption of mustard via the CDPK signaling pathway.